ClickHouse store folder grows uncontrollably and is not cleaned up

[thibautLedz]

Hello team,

I'm self-hosting Plausible CE using Docker Compose (with the official setup). Plausible 3.0.1. I’ve noticed that the plausible-ce_event-data volume (used by ClickHouse) keeps growing in size, even though:

• The events_v2 table only holds about 700k rows.
• system.parts reports only a few dozen active parts, totaling ~10 MiB on disk.
• Yet, the underlying ClickHouse store folder is currently over 44 GiB:

/var/lib/docker/volumes/plausible-ce_event-data/_data/store/0bb/0bbbeb02-... → 44G causing NO LEFT SPACE ON DEVICE

After investigation:

• Many large part folders (several hundred MB to >1 GiB each) exist on disk but do not correspond to any active part in system.parts.
• OPTIMIZE TABLE ... FINAL does not seem to clear them.
• These parts appear to be dangling / orphaned, possibly due to merges being aborted or unreclaimed data.
• The files continue being updated (file timestamps) even though they're not referenced by any active table part.
• This leads to disk exhaustion over time on relatively small VPS setups.

---

Steps I've taken:

• Ran ClickHouse queries to list active parts and their sizes
• Compared actual files in /store with system.parts
• Verified no active merges in system.merges
• Tried OPTIMIZE TABLE ... FINAL
• Ensured no secondary container is writing to the volume

---

Questions

• Is there anything in Plausible’s setup that might prevent ClickHouse from garbage collecting those parts?
• Could you recommend a safe cleanup strategy or confirm if manual deletion of those folders is acceptable?

---

Thanks a lot for this awesome project. I'd be happy to provide logs or help debug further if needed.

Best,
Thibaut

[thibautLedz]

Chatgpt suggests me to add a new config file and play with merge_tree options :

plausible-ce/clickhouse/merge_tree_cleanup.xml

<clickhouse>
    <merge_tree>
        ...
    </merge_tree>
</clickhouse>

plausible-ce/docker-compose.yml

volumes:
  - ./clickhouse/merge_tree_cleanup.xml:/etc/clickhouse-server/config.d/merge_tree_cleanup.xml:ro

[e11bits]

I had to stop using the selfhosted Plausible CE for that reason.

[spammads]

Did you find a solution @thibautLedz ?
I deleted a big folder and it seems this did not have any side-effects. But. Yeah. Probably not the best approach to delete random filesystem-folders …

[thibautLedz]

I used chatGPT to help me compare active parts and dead parts in the store folder and delete all inactives. But it is a temporary solution. Folder is still growing

[spammads]

ok. thanks for the update.
i now set

<merge_tree>
    <allow_experimental_replacing_merge_with_cleanup>1</allow_experimental_replacing_merge_with_cleanup>
</merge_tree>

and will have a look if this keeps the folder-size a bit under control.